AFL chief executive Gillon McLachlan says the league will respect confidentiality agreements in sexual harassment cases as long as the issue has been resolved between the two parties.
Fremantle hit the headlines earlier this month when it was reported an official made a secret payment to a former junior staffer to settle an alleged sexual harassment complaint.
The AFL's integrity unit investigated the harassment claims and found no further action was needed.
The Fremantle official at the centre of the storm has remained anonymous.
The murky issue of hush payments was raised when McLachlan fronted the media in Perth on Friday.
Without wanting to comment directly on the situation at Fremantle, he said it was important for confidentiality agreements to be honoured when the circumstances warranted.
"What the core part of the policy is ... is actually resolving the issue between the complainant and the person who they are making the allegation against," McLachlan said.
"It's entirely appropriate and part of the policy for it to be confidential.
"There's a wide series of options available for getting resolution. There are many cases that are resolved confidentially.
"That's one of the core tenants of the policy - where possible and where appropriate, the confidentiality remains because it's resolving the issue at hand between the two parties rather than actually being something for public debate.
"I think it's unfortunate when it comes out. Unfortunate for the complainant and the person who is being complained against."
Earlier this week, Port Adelaide president David Koch slammed the AFL over its Sam Powell-Pepper investigation.
Koch said Power-Pepper was a victim of the AFL's attempts to rebuild its reputation with women following the resignations of league executives Simon Lethlean and Richard Simkiss over their affairs with junior colleagues.
Powell-Pepper was slapped with a three-match ban over his late-night drunken behaviour, which the AFL said also included engaging in "inappropriate contact with a female".
Koch accused the AFL of "railroading a kid and trying to rebuild their reputation".
McLachlan said there was no bad blood between the AFL and Port Adelaide over the handling of the investigation.
"I think David was emotional and clearly feels he's protecting his player and his club," McLachlan said.
"I completely disagree and reject some of the things he said.
"Football's a passionate, emotional business, and I don't take any of it personally."
